search

YeoLab / gscripts

General Use Scripts and Helper functions
MIT License
17 stars 18 forks source link

rna_seq_scala fails at submit_miso_pipeline.py #48

Closed LeenMachine closed 9 years ago

LeenMachine commented 9 years ago

ERROR 10:43:06,336 FunctionEdge - Error: submit_miso_pipeline.py '--bam' '/oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.bam' '--sample-id' 'D3-SC_GAATTCGT-TATAGCCT_L003_R1' '--genome' 'mm10' '--do-not-submit' '--output-sh' 'D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso.sh' && 'sh' 'D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso.sh' && 'touch' '/oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso'
ERROR 10:43:06,353 FunctionEdge - Contents of /oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso.out: Wrote miso script for sample "D3-SC_GAATTCGT-TATAGCCT_L003_R1": D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso.sh MISO psi failed on event type: SE Nodes: tscc-3-51 ERROR 10:43:06,362 FunctionEdge - Error: count_tags.py '--bam_file' '/oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.bam' '--annotation_file' 'none' '--flip' 'flipped' '--out_file' '/oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.count'
ERROR 10:43:06,371 FunctionEdge - Contents of /oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.count.out: Traceback (most recent call last): File "/projects/ps-yeolab/software/anaconda/bin/count_tags.py", line 6, in exec(compile(open(file).read(), file, 'exec')) File "/home/ljamal/gscripts/gscripts/rnaseq/count_tags.py", line 204, in annotation = options.annotation, jxns_file=options.jxns) File "/home/ljamal/gscripts/gscripts/rnaseq/count_tags.py", line 163, in count_tags genes = count_to_regions(annotation) File "/home/ljamal/gscripts/gscripts/rnaseq/count_tags.py", line 53, in count_to_regions with open(annotation, 'r') as gene_file: IOError: [Errno 2] No such file or directory: 'none'

gpratt commented 9 years ago

There isn't a mm10 annotation for count tags.

I suggest you post-process with featureCounts ( http://bioinf.wehi.edu.au/featureCounts/) or use sailfish

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Fri, Dec 5, 2014 at 10:53 AM, Leen notifications@github.com wrote:

ERROR 10:43:06,336 FunctionEdge - Error: submit_miso_pipeline.py '--bam' '/oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.bam' '--sample-id' 'D3-SC_GAATTCGT-TATAGCCT_L003_R1' '--genome' 'mm10' '--do-not-submit' '--output-sh' ' D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso.sh' && 'sh' ' D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso.sh' && 'touch' '/oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso'

ERROR 10:43:06,353 FunctionEdge - Contents of /oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso.out: Wrote miso script for sample "D3-SC_GAATTCGT-TATAGCCT_L003_R1": D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.miso.sh MISO psi failed on event type: SE Nodes: tscc-3-51 ERROR 10:43:06,362 FunctionEdge - Error: count_tags.py '--bam_file' '/oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.bam' '--annotation_file' 'none' '--flip' 'flipped' '--out_file' '/oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.count'

ERROR 10:43:06,371 FunctionEdge - Contents of /oasis/tscc/scratch/ljamal/a2b1/D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz.sorted.rg.count.out: Traceback (most recent call last): File "/projects/ps-yeolab/software/anaconda/bin/count_tags.py", line 6, in exec(compile(open(file).read(), file, 'exec')) File "/home/ljamal/gscripts/gscripts/rnaseq/count_tags.py", line 204, in annotation = options.annotation, jxns_file=options.jxns) File "/home/ljamal/gscripts/gscripts/rnaseq/count_tags.py", line 163, in count_tags genes = count_to_regions(annotation) File "/home/ljamal/gscripts/gscripts/rnaseq/count_tags.py", line 53, in count_to_regions with open(annotation, 'r') as gene_file: IOError: [Errno 2] No such file or directory: 'none'

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/48.

olgabot commented 9 years ago

I only see the error message for count_tags, where's the error message for miso?

olgabot commented 9 years ago

I suggest you post-process with featureCounts ( http://bioinf.wehi.edu.au/featureCounts/) or use sailfish

@gpratt , wouldn't that require rewriting the pipeline or writing a separate scala script for that?

gpratt commented 9 years ago

It means making a new annotation for mm10. I think countTags should be at its end of life so I'm not going to make it. If we really want to keep using it we can make a new annotation, but for straight counting featureCounts does almost exactly the same stuff and is faster.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Fri, Dec 5, 2014 at 11:14 AM, Olga Botvinnik notifications@github.com wrote:

@gpratt https://github.com/gpratt , wouldn't that require rewriting the pipeline or writing a separate scala script for that?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/48#issuecomment-65839192.

LeenMachine commented 9 years ago

@olgabot, the first window of this issue, line 2 is where miso fails

LeenMachine commented 9 years ago

Here is what one of the miso.out files looks like:

Wrote miso script for sample "D1-SC_GAGATTCC_L002_R1": D1-SC_GAGATTCC_L002_R1.fastq.gz.sorted.rg.miso.sh MISO psi failed on event type: SE Nodes: tscc-3-40

olgabot commented 9 years ago

Wrote miso script for sample "D1-SC_GAGATTCC_L002_R1": D1-SC_GAGATTCC_L002_R1.fastq.gz.sorted.rg.miso.sh

Can you show the output of that script?

There should also be a miso/ directory with the sample names, then different splice types within the sample. Can you show the output of ls miso/D1-SC/SE (if D1-SC1 is the sample id, otherwise use the real sample id. I just guessed here)

LeenMachine commented 9 years ago

Installed pysam but miso looks like it is still failing

ERROR 14:16:26,914 FunctionEdge - Error: submit_miso_pipeline.py  '--bam' '/oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C09_TAAGGCGA-CTCTCTAT.fastq.gz.sorted.rg.bam'  '--sample-id' 'CarD15-2_C09_TAAGGCGA-CTCTCTAT'  '--genome' 'hg19'  '--do-not-submit'  '--output-sh' 'CarD15-2_C09_TAAGGCGA-CTCTCTAT.fastq.gz.sorted.rg.miso.sh'  &&  'sh' 'CarD15-2_C09_TAAGGCGA-CTCTCTAT.fastq.gz.sorted.rg.miso.sh'  &&  'touch' '/oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C09_TAAGGCGA-CTCTCTAT.fastq.gz.sorted.rg.miso'
ERROR 14:16:26,931 FunctionEdge - Contents of /oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C09_TAAGGCGA-CTCTCTAT.fastq.gz.sorted.rg.miso.out:
discarding /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/ljamal/bin to PATH
discarding /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/ljamal/bin to PATH
Wrote miso script for sample "CarD15-2_C09_TAAGGCGA-CTCTCTAT": CarD15-2_C09_TAAGGCGA-CTCTCTAT.fastq.gz.sorted.rg.miso.sh
MISO psi failed on event type: SE
LeenMachine commented 9 years ago

Using hg19:

ERROR 14:34:59,139 FunctionEdge - Error: submit_miso_pipeline.py  '--bam' '/oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.bam'  '--sample-id' 'CarD15-2_C10_GCTACGCT-CTCTCTAT'  '--genome' 'hg19'  '--do-not-submit'  '--output-sh' 'CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.miso.sh'  &&  'sh' 'CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.miso.sh'  &&  'touch' '/oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.miso'  
ERROR 14:34:59,154 FunctionEdge - Contents of /oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.miso.out:
discarding /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/ljamal/bin to PATH
discarding /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/ljamal/bin to PATH
olgabot commented 9 years ago

can you show the output of "tail miso///psi.err"? I can't quite see from here what the error is.

On Fri Dec 05 2014 at 2:36:05 PM Leen notifications@github.com wrote:

Using hg19:

ERROR 14:34:59,139 FunctionEdge - Error: submit_miso_pipeline.py '--bam' '/oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.bam' '--sample-id' 'CarD15-2_C10_GCTACGCT-CTCTCTAT' '--genome' 'hg19' '--do-not-submit' '--output-sh' 'CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.miso.sh' && 'sh' 'CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.miso.sh' && 'touch' '/oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.miso' ERROR 14:34:59,154 FunctionEdge - Contents of /oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C10_GCTACGCT-CTCTCTAT.fastq.gz.sorted.rg.miso.out: discarding /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/bin from PATH prepending /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/ljamal/bin to PATH discarding /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/bin from PATH prepending /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/ljamal/bin to PATH

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/48#issuecomment-65865783.

LeenMachine commented 9 years ago

When I looked at the tail of psi.err, it wanted me to install misopy

I tried to install misopy

(ljamal)[ljamal@tscc-login2 SE]$ conda install misopy
Fetching package metadata: ..
Error: No packages found in current linux-64 channels matching: misopy

You can search for this package on Binstar with

    binstar search -t conda misopy

You may need to install the Binstar command line client with

    conda install binstar
(ljamal)[ljamal@tscc-login2 SE]$ binstar search -t conda misopy
Using binstar api site https://api.binstar.org
Run 'binstar show <USER/PACKAGE>' to get more details:
No packages found
     Name                      |  Version | Package Types   | Platforms      
     ------------------------- |   ------ | --------------- | ---------------
Found 0 packages
(ljamal)[ljamal@tscc-login2 SE]$ conda install misopy
Fetching package metadata: ..
Error: No packages found in current linux-64 channels matching: misopy

You can search for this package on Binstar with

    binstar search -t conda misopy

You may need to install the Binstar command line client with

    conda install binstar

i installed binstar and tried again. You are looking at the output above

LeenMachine commented 9 years ago

I just tried pip install... I'm not sure if it is working. It is giving me a lot of warnings

LeenMachine commented 9 years ago

pip install successfully installed misopy. Trying to run the pipeline again to look for errors.

LeenMachine commented 9 years ago

Miso now runs

olgabot commented 9 years ago

Ok great. Sorry about that - I'll make sure to add pysam and misopy to the base environment.

yarden commented 9 years ago

BTW: conda install misopy should work now

olgabot commented 9 years ago

Fantastic! Thanks, Yarden!

On Mon, Mar 16, 2015 at 3:40 PM Yarden Katz notifications@github.com wrote:

BTW: conda install misopy should work now

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/48#issuecomment-81970242.

yarden commented 9 years ago

PS For some reason it looks like it's registered on osx only... I am not sure why, I find binstar/conda very confusing, but it could be made to work on Linux too